3u5m

Crystal structure of TRIM33 PHD-Bromo in the free state

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase TRIM33

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ZINC ION × 2	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRI33_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–207； UniProt 882–1087 Author chain B； PDBConstruct 2–207； UniProt 882–1087 Author chain C； PDBConstruct 2–207； UniProt 882–1087 Author chain D； PDBConstruct 2–207； UniProt 882–1087 Author chain E； PDBConstruct 2–207； UniProt 882–1087 Author chain F； PDBConstruct 2–207； UniProt 882–1087 Author chain G； PDBConstruct 2–207； UniProt 882–1087 Author chain H； PDBConstruct 2–207； UniProt 882–1087 Author chain I； PDBConstruct 2–207； UniProt 882–1087 Author chain J； PDBConstruct 2–207； UniProt 882–1087 Author chain K； PDBConstruct 2–207； UniProt 882–1087 Author chain L； PDBConstruct 2–207； UniProt 882–1087

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3u5m
Deposition date deposition_date	2011-10-11
Structure title title	Crystal structure of TRIM33 PHD-Bromo in the free state
Keywords keywords	TRIM33, PHD, Bromodomain, TGF-beta, epigenetics, histone, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3u5m__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3u5m__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u5m__assembly_9__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.11 Å
Rg (electron density)	17.03 Å
Total Rg	18.13 Å
Atom count	1401
Residues	173
Excluded volume	25236 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u5m__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u5m__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3u5m__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3u5m__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3u5m__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3u5m__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3u5m__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3u5m__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3u5m__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3u5m__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3u5m__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3u5m__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase TRIM33
Molecular weight formula_weight	23830.3 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	17117

SDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	3u5mA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mJ01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mJ02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mK02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5mL01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5mL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	79.527 Å
Unit-cell length b length_b	79.781 Å
Unit-cell length c length_c	134.160 Å
Unit-cell angle α angle_alpha	89.90 °
Unit-cell angle β angle_beta	89.96 °
Unit-cell angle γ angle_gamma	59.97 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.080 Å
Low-resolution limit resolution_low	27.360 Å
R factor r_factor	0.2106
R_work r_work	0.2074
R_free r_free	0.2935

Crystal structure of TRIM33 PHD-Bromo in the free state

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase TRIM33

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3u5m__assembly_9__model_1

3u5m__assembly_9__model_1 | I(q)

3u5m__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of TRIM33 PHD-Bromo in the free state

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase TRIM33

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3u5m__assembly_9__model_1

3u5m__assembly_9__model_1 | I(q)

3u5m__assembly_9__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)